Fix chain ID handling in make_ndx

The tool was still using the oldest possible way to read in structure
files, leading to issues with the chain IDs being overwritten and
replaced with the default id.

Fixes #3070
Refs #3113

Change-Id: I25112103a043d0266fe64c7619fe8e4abc56ffa5

diff --git a/docs/release-notes/2019/2019.4.rst b/docs/release-notes/2019/2019.4.rst
index 087c8c32f1197ef6760f98f18af8717a6c754d88..ec0a89d4fc20f5152a5efcf81240a610ccc97230 100644 (file)
--- a/docs/release-notes/2019/2019.4.rst
+++ b/docs/release-notes/2019/2019.4.rst
@@ -128,6 +128,14 @@ indices in the index file.
 
 :issue:`3107`
 
+Made gmx make_ndx keep chain IDs
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+Old style structure file reading caused the chain IDs to be overwritten with
+default values.
+
+:issue:`3070`
+
 Fixes that affect portability
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

diff --git a/src/gromacs/gmxana/gmx_make_ndx.cpp b/src/gromacs/gmxana/gmx_make_ndx.cpp
index a1ece34082621009d40c838364865a44fc426472..f479eefd806a8db5474cb632a82a742b33f8dd1b 100644 (file)
--- a/src/gromacs/gmxana/gmx_make_ndx.cpp
+++ b/src/gromacs/gmxana/gmx_make_ndx.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -47,6 +47,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/index.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/arraysize.h"
 #include "gromacs/utility/cstringutil.h"
@@ -1557,7 +1558,7 @@ int gmx_make_ndx(int argc, char *argv[])
     const char       *ndxoutfile;
     gmx_bool          bNatoms;
     int               j;
-    t_atoms          *atoms;
+    t_atoms           atoms;
     rvec             *x, *v;
     int               ePBC;
     matrix            box;
@@ -1586,23 +1587,23 @@ int gmx_make_ndx(int argc, char *argv[])
         gmx_fatal(FARGS, "No input files (structure or index)");
     }
 
+    gmx_mtop_t mtop;
     if (stxfile)
     {
-        t_topology *top;
-        snew(top, 1);
+        bool haveFullTopology = false;
         fprintf(stderr, "\nReading structure file\n");
-        read_tps_conf(stxfile, top, &ePBC, &x, &v, box, FALSE);
-        atoms = &top->atoms;
-        if (atoms->pdbinfo == nullptr)
+        readConfAndTopology(stxfile, &haveFullTopology, &mtop,
+                            &ePBC, &x, &v, box);
+        atoms = gmx_mtop_global_atoms(&mtop);
+        if (atoms.pdbinfo == nullptr)
         {
-            snew(atoms->pdbinfo, atoms->nr);
+            snew(atoms.pdbinfo, atoms.nr);
         }
-        natoms  = atoms->nr;
+        natoms  = atoms.nr;
         bNatoms = TRUE;
     }
     else
     {
-        atoms = nullptr;
         x     = nullptr;
     }
 
@@ -1631,7 +1632,7 @@ int gmx_make_ndx(int argc, char *argv[])
     else
     {
         snew(gnames, 1);
-        analyse(atoms, block, &gnames, FALSE, TRUE);
+        analyse(&atoms, block, &gnames, FALSE, TRUE);
     }
 
     if (!bNatoms)
@@ -1640,7 +1641,7 @@ int gmx_make_ndx(int argc, char *argv[])
         printf("Counted atom numbers up to %d in index file\n", natoms);
     }
 
-    edit_index(natoms, atoms, x, block, &gnames, bVerbose);
+    edit_index(natoms, &atoms, x, block, &gnames, bVerbose);
 
     write_index(ndxoutfile, block, gnames, bDuplicate, natoms);